3GDB | pdb_00003gdb

Crystal structure of Spr0440 glycoside hydrolase domain, Endo-D from Streptococcus pneumoniae R6

• PDB DOI: https://doi.org/10.2210/pdb3GDB/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pneumoniae R6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-24 Released: 2009-03-17 
• Deposition Author(s): Jiang, Y.-L., Frolet, C., Di-guilmi, A.-M., Zhou, C.-Z., Vernet, T., Chen, Y.-X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.204 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal structure of Spr0440 glycoside hydrolase domain, Endo-D from Streptococcus pneumoniae R6

Jiang, Y.-L., Frolet, C., Di-guilmi, A.-M., Zhou, C.-Z., Vernet, T., Chen, Y.-X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 104.48 kDa 
• Atom Count: 5,805 
• Modeled Residue Count: 634 
• Deposited Residue Count: 937 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein spr0440	A	937	Streptococcus pneumoniae R6	Mutation(s): 0  Gene Names: spr0440 EC: 3.2.1.96
UniProt
Find proteins for Q8CZ52 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8CZ52  Go to UniProtKB:  Q8CZ52

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ACY	B [auth A], C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.204 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.14	α = 90
b = 59.06	β = 110.27
c = 94.89	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SOLVE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Jiang, Y.-L., Frolet, C., Di-guilmi, A.-M., Zhou, C.-Z., Vernet, T., Chen, Y.-X.

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations